Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 3.15788216065901e-05 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:45779136A>TN/A show variant in all transcripts   IGV
HGNC symbol SACM1L
Ensembl transcript ID ENST00000389061
Genbank transcript ID NM_014016
UniProt peptide Q9NTJ5
alteration type single base exchange
alteration region CDS
DNA changes c.1301A>T
cDNA.1505A>T
g.48589A>T
AA changes Y434F Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 434
frameshift no
known variant Reference ID: rs1468542
databasehomozygous (T/T)heterozygousallele carriers
1000G79711521949
ExAC22561-1235510206
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.9211
2.9871
(flanking)0.9811
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased48591wt: 0.27 / mu: 0.50wt: TTTACAAAAATGGTA
mu: TTTTCAAAAATGGTA		 TACA|aaaa
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      434KLEEQDEFEKIYKNAWADNANACA
mutated  all conserved    434KLEEQDEFEKIFKNAWADNANAC
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002130  454KLEEQDEFEKIYKNAWADNANAC
Fcatus  all identical  ENSFCAG00000006822  434KLEEQHDFEKIYKNAWADNANAC
Mmusculus  all identical  ENSMUSG00000025240  434KLEEQDEFEKTYKNAWADNANAC
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000003634  434RIEEQAEFEKIYKNAWADNANAC
Drerio  no homologue    
Dmelanogaster  all conserved  FBgn0035195  433KVEHASDIFESIFKGVWADNADLV
Celegans  all conserved  F30A10.6  445KVQDIPLLEDAFKQMWADNGDEC
Xtropicalis  all identical  ENSXETG00000011975  230RIEEQIQFEKIYKNAAWADNAN
protein features
start (aa)end (aa)featuredetails 
122451DOMAINSAC.lost
456456MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
521541TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
549569TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1764 / 1764
position (AA) of stopcodon in wt / mu AA sequence 588 / 588
position of stopcodon in wt / mu cDNA 1968 / 1968
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 205 / 205
chromosome 3
strand 1
last intron/exon boundary 1832
theoretical NMD boundary in CDS 1577
length of CDS 1764
coding sequence (CDS) position 1301
cDNA position
(for ins/del: last normal base / first normal base)		 1505
gDNA position
(for ins/del: last normal base / first normal base)		 48589
chromosomal position
(for ins/del: last normal base / first normal base)		 45779136
original gDNA sequence snippet AGATGAATTTGAGAAGATTTACAAAAATGGTAGGTCATTTC
altered gDNA sequence snippet AGATGAATTTGAGAAGATTTTCAAAAATGGTAGGTCATTTC
original cDNA sequence snippet AGATGAATTTGAGAAGATTTACAAAAATGCCTGGGCTGACA
altered cDNA sequence snippet AGATGAATTTGAGAAGATTTTCAAAAATGCCTGGGCTGACA
wildtype AA sequence MATAAYEQLK LHITPEKFYV EACDDGADDV LTIDRVSTEV TLAVKKDVPP SAVTRPIFGI
LGTIHLVAGN YLIVITKKIK VGEFFSHVVW KATDFDVLSY KKTMLHLTDI QLQDNKTFLA
MLNHVLNVDG FYFSTTYDLT HTLQRLSNTS PEFQEMSLLE RADQRFVWNG HLLRELSAQP
EVHRFALPVL HGFITMHSCS INGKYFDWIL ISRRSCFRAG VRYYVRGIDS EGHAANFVET
EQIVHYNGSK ASFVQTRGSI PVFWSQRPNL KYKPLPQISK VANHMDGFQR HFDSQVIIYG
KQVIINLINQ KGSEKPLEQT FATMVSSLGS GMMRYIAFDF HKECKNMRWD RLSILLDQVA
EMQDELSYFL VDSAGQVVAN QEGVFRSNCM DCLDRTNVIQ SLLARRSLQA QLQRLGVLHV
GQKLEEQDEF EKIYKNAWAD NANACAKQYA GTGALKTDFT RTGKRTHLGL IMDGWNSMIR
YYKNNFSDGF RQDSIDLFLG NYSVDELESH SPLSVPRDWK FLALPIIMVV AFSMCIICLL
MAGDTWTETL AYVLFWGVAS IGTFFIILYN GKDFVDAPRL VQKEKID*
mutated AA sequence MATAAYEQLK LHITPEKFYV EACDDGADDV LTIDRVSTEV TLAVKKDVPP SAVTRPIFGI
LGTIHLVAGN YLIVITKKIK VGEFFSHVVW KATDFDVLSY KKTMLHLTDI QLQDNKTFLA
MLNHVLNVDG FYFSTTYDLT HTLQRLSNTS PEFQEMSLLE RADQRFVWNG HLLRELSAQP
EVHRFALPVL HGFITMHSCS INGKYFDWIL ISRRSCFRAG VRYYVRGIDS EGHAANFVET
EQIVHYNGSK ASFVQTRGSI PVFWSQRPNL KYKPLPQISK VANHMDGFQR HFDSQVIIYG
KQVIINLINQ KGSEKPLEQT FATMVSSLGS GMMRYIAFDF HKECKNMRWD RLSILLDQVA
EMQDELSYFL VDSAGQVVAN QEGVFRSNCM DCLDRTNVIQ SLLARRSLQA QLQRLGVLHV
GQKLEEQDEF EKIFKNAWAD NANACAKQYA GTGALKTDFT RTGKRTHLGL IMDGWNSMIR
YYKNNFSDGF RQDSIDLFLG NYSVDELESH SPLSVPRDWK FLALPIIMVV AFSMCIICLL
MAGDTWTETL AYVLFWGVAS IGTFFIILYN GKDFVDAPRL VQKEKID*
speed 1.32 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project